Contacts of the strand formed by residues 550 - 555 (chain A) in PDB entry 4FYT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 550 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A TRP* 3.6 25.8 - - + -
549A PHE* 1.3 97.2 - - + +
551A VAL* 1.3 58.9 + - - +
552A ILE* 4.0 19.5 - - + -
563A GLN* 4.1 9.6 - - + +
564A GLU 3.2 11.7 - - - +
584A TRP* 3.6 25.1 - - + -
586A VAL* 4.3 7.4 - - + -
629A TYR 3.9 2.0 - - - +
630A TYR* 3.4 14.8 - - + +
631A ARG 3.2 21.1 + - - -
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A PRO* 1.3 72.6 - - - +
552A ILE* 1.3 66.6 - - - +
553A THR* 3.9 18.0 + - - +
562A SER 3.6 1.2 - - - +
563A GLN* 3.3 5.2 - - - -
564A GLU* 2.9 50.6 + - + +
566A PHE* 3.9 28.9 - - + +
631A ARG* 3.4 15.3 - - + +
633A ASN* 4.1 6.3 - - + +
668A LEU* 3.7 25.6 - - + -
673A LYS* 4.1 11.4 - - + -
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Residues in contact with ILE 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A PRO* 4.0 15.3 - - + -
551A VAL* 1.3 73.5 - - - +
553A THR* 1.3 61.5 + - - +
561A LEU* 4.2 15.9 - - + -
562A SER 3.2 5.8 - - - +
563A GLN* 3.6 25.4 - - + -
586A VAL* 4.3 9.6 - - + -
588A ILE* 4.1 12.8 - - + -
602A LEU* 3.8 12.1 - - + -
622A LEU* 4.0 25.1 - - + -
630A TYR* 3.5 32.3 - - + -
631A ARG 2.9 9.6 + - - +
632A VAL* 3.3 7.0 - - - +
633A ASN 2.9 24.0 + - - +
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Residues in contact with THR 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A VAL* 3.9 12.4 + - - +
552A ILE* 1.3 73.5 - - - +
554A VAL* 1.3 69.1 + - - +
555A ASP 4.1 0.3 + - - -
560A THR 3.8 0.5 - - - +
561A LEU* 3.3 5.1 - - - -
562A SER* 2.8 46.7 + - - +
564A GLU* 6.0 0.5 - - - +
633A ASN* 3.3 31.5 + - + +
634A TYR 4.9 3.4 - - - +
673A LYS* 5.8 1.6 - - - +
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ILE* 4.6 0.9 - - + +
553A THR* 1.3 78.0 - - - +
555A ASP* 1.3 62.4 + - - +
556A THR* 3.8 22.7 - - + -
560A THR 3.4 6.1 - - - +
561A LEU* 3.5 18.2 - - + -
612A PHE* 3.9 27.6 - - + +
620A VAL* 4.9 1.1 - - + -
622A LEU* 3.7 28.7 - - + -
632A VAL* 4.3 2.9 - - + -
633A ASN 2.8 16.9 + - - +
634A TYR* 3.4 15.1 - - + -
635A ASP* 3.0 27.4 + - - +
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Residues in contact with ASP 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A THR 4.1 0.4 + - - -
554A VAL* 1.3 73.5 - - - +
556A THR* 1.3 58.2 + - - +
557A SER* 3.0 26.6 + - - -
558A THR* 3.6 15.8 + - - +
559A GLY* 2.8 25.6 + - - -
560A THR* 2.9 31.1 + - - +
635A ASP* 3.9 12.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il